1L3S

Crystal Structure of Bacillus DNA Polymerase I Fragment complexed to 9 base pairs of duplex DNA.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations

Johnson, S.J., Taylor, J.S., Beese, L.S.

(2003) Proc.Natl.Acad.Sci.USA 100: 3895-3900

  • DOI: 10.1073/pnas.0630532100
  • Primary Citation of Related Structures:  
  • Also Cited By: 1NKE, 1NKC, 1NKB, 1NK9, 1NK8, 1NK7, 1NK6, 1NK5, 1NK4, 1NK0, 1NJZ, 1NJY, 1NJX, 1NJW

  • PubMed Abstract: 

    • DNA polymerases replicate DNA by adding nucleotides to a growing primer strand while avoiding frameshift and point mutations. Here we present a series of up to six successive replication events that were obtained by extension of a primed template dir ...

    DNA polymerases replicate DNA by adding nucleotides to a growing primer strand while avoiding frameshift and point mutations. Here we present a series of up to six successive replication events that were obtained by extension of a primed template directly in a crystal of the thermostable Bacillus DNA polymerase I. The 6-bp extension involves a 20-A translocation of the DNA duplex, representing the largest molecular movement observed in a protein crystal. In addition, we obtained the structure of a "closed" conformation of the enzyme with a bound triphosphate juxtaposed to a template and a dideoxy-terminated primer by constructing a point mutant that destroys a crystal lattice contact stabilizing the wild-type polymerase in an "open" conformation. Together, these observations allow many of the steps involved in DNA replication to be observed in the same enzyme at near atomic detail. The successive replication events observed directly by catalysis in the crystal confirm the general reaction sequence deduced from observations obtained by using several other polymerases and further refine critical aspects of the known reaction mechanism, and also allow us to propose new features that concern the regulated transfer of the template strand between a preinsertion site and an insertion site. We propose that such regulated transfer is an important element in the prevention of frameshift mutations in high-fidelity DNA polymerases. The ability to observe processive, high-fidelity replication directly in a crystal establishes this polymerase as a powerful model system for mechanistic studies in which the structural consequences of mismatches and DNA adducts are observed.

    Related Citations: 
    • Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution
      Kiefer, J.R.,Mao, C.,Hansen, C.J.,Basehore, S.L.,Hogrefe, H.H.,Braman, J.C.,Beese, L.S.
      (1997) Structure 5: 95
    • Visualizing DNA Replication in a Catalytically Active Bacillus DNA Polymerase Crystal
      Kiefer, J.R.,Mao, C.,Braman, J.C.,Beese, L.S.
      (1998) Nature 391: 304

    Organizational Affiliation: 

    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA Polymerase I
A
580Geobacillus stearothermophilusMutation(s): 0 
Gene Names: polA (pol)
EC: 2.7.7.7
Find proteins for P52026 (Geobacillus stearothermophilus)
Go to UniProtKB:  P52026
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*G)-3'B9N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*A*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'C16N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC
Download SDF File 
Download CCD File 
A
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.289α = 90.00
b = 93.254β = 90.00
c = 106.292γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance